Single-cell RNA-seq of the rare virosphere reveals the native hosts of giant viruses in the marine environment

Giant viruses (phylum Nucleocytoviricota) are globally distributed in aquatic ecosystems. They play significant roles as evolutionary drivers of eukaryotic plankton and regulators of global biogeochemical cycles. However, we lack knowledge about their native hosts, hindering our understanding of their lifecycle and ecological importance. Here, we used single-cell RNAseq and samples from an induced E. huxleyi bloom during a mesocosm experiment to link giant viruses with their protist hosts. We observe active giant virus infections in multiple host lineages, including members of the algal groups Chrysophycae and Prymnesiophycae, as well as heterotrophic flagellates in the class Katablepharidaceae. Katablepharids were infected with a rare Imitevirales-07 giant virus lineage expressing cell fate regulation genes. Analysis of the temporal dynamics of this host-virus interaction indicated a role for the Imitevirales-07 in the collapse of the host Katablepharid population. Our results demonstr..., Mesocosm core setup and sampling procedure
Samples were obtained during the AQUACOSM VIMS-Ehux mesocosm experiment in Raunefjorden near Bergen, Norway (60°16′11N; 5°13′07E), in May 2018. Seven bags were filled with 11m3 water from the fjord, containing natural plankton communities. Algal blooms were induced by nutrient addition and monitored for 24 days, as previously described23. 10 samples were collected from four bags, as follows: From bag 3, on days 15 and 20 (named B3T15, B3T20 correspondingly). From bag 4, on days 13, 15,19, and 20 (named B4T13, B4T15, B4T19, and B4T20, correspondingly). From bag 6, on day 17 (named B6T17). From bag 7, on days 16, 17, and 18 (named B7T16, B7T17, and B7T18, correspondingly).
Samples were initially filtered as follows: 2 liters of water were filtered with a 20 µm mesh and collected in a glass bottle. The cells were then concentrated through gentle gravity filtration on a 3 µm polycarbonate filter (Whatman), mounted on a reusable bottle top filter h..., , # Single-cell RNA-seq of the rare virosphere reveals the native hosts of giant viruses in the marine environment

Supplementary Files used in the project. These are the main intermediate files that can help reproduce the data. For a detail description on how to reproduce these files and using them, Go to the GitHub site: [https://github.com/vardilab/host-virus-pairing](https://github.com/vardilab/host-virus-pairing)

## Description of the data and file structure

Fromm_2023_Data_Availability
Sequences
GVDB.markergenes.90.fna # De-duplicated database of NCLDV marker genes
Transcripts_Cells_Ehux-EhV.95.fasta # The host-virus reference, based on the single-cell transcriptomes of infected cells, to which we added genes from EhV and E. huxleyi.
Transcripts_Katablepharidacea.fasta # Transcripts assembled from a highly infected subpopulation of Katablepharidacea

Blast_results
first_cells.transcripts.edit.metaPR2.csv # Blastn results of singl...